rs58582188
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001002295.2(GATA3):c.*266dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00812 in 505,786 control chromosomes in the GnomAD database, including 39 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.013 ( 25 hom., cov: 32)
Exomes 𝑓: 0.0061 ( 14 hom. )
Consequence
GATA3
NM_001002295.2 3_prime_UTR
NM_001002295.2 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.42
Genes affected
GATA3 (HGNC:4172): (GATA binding protein 3) This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is an important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia. [provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 10-8074288-A-AT is Benign according to our data. Variant chr10-8074288-A-AT is described in ClinVar as [Likely_benign]. Clinvar id is 1201835.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0128 (1948/151792) while in subpopulation AFR AF= 0.0298 (1233/41386). AF 95% confidence interval is 0.0284. There are 25 homozygotes in gnomad4. There are 918 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1948 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GATA3 | NM_001002295.2 | c.*266dupT | 3_prime_UTR_variant | 6/6 | ENST00000379328.9 | NP_001002295.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GATA3 | ENST00000379328.9 | c.*266dupT | 3_prime_UTR_variant | 6/6 | 1 | NM_001002295.2 | ENSP00000368632.3 | |||
GATA3 | ENST00000346208.4 | c.*266dupT | 3_prime_UTR_variant | 6/6 | 1 | ENSP00000341619.3 |
Frequencies
GnomAD3 genomes AF: 0.0128 AC: 1947AN: 151674Hom.: 25 Cov.: 32
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GnomAD4 exome AF: 0.00610 AC: 2159AN: 353994Hom.: 14 Cov.: 0 AF XY: 0.00591 AC XY: 1076AN XY: 182164
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GnomAD4 genome AF: 0.0128 AC: 1948AN: 151792Hom.: 25 Cov.: 32 AF XY: 0.0124 AC XY: 918AN XY: 74190
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 06, 2019 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at